How To Install python-treetime-examples on Ubuntu 18.04
Introduction
In this tutorial we learn how to install python-treetime-examples on Ubuntu 18.04.
What is python-treetime-examples
python-treetime-examples is:
TreeTime provides routines for ancestral sequence reconstruction and the maximum likelihoo inference of molecular-clock phylogenies, i.e., a tree where all branches are scaled such that the locations of terminal nodes correspond to their sampling times and internal nodes are placed at the most likely time of divergence.
TreeTime aims at striking a compromise between sophisticated probabilistic models of evolution and fast heuristics. It implements GTR models of ancestral inference and branch length optimization, but takes the tree topology as given. To optimize the likelihood of time-scaled phylogenies, treetime uses an iterative approach that first infers ancestral sequences given the branch length of the tree, then optimizes the positions of unconstraine d nodes on the time axis, and then repeats this cycle. The only topology optimization are (optional) resolution of polytomies in a way that is most (approximately) consistent with the sampling time constraints on the tree. The package is designed to be used as a stand-alone tool or as a library used in larger phylogenetic analysis workflows.
Features
- ancestral sequence reconstruction (marginal and joint maximum likelihood)
- molecular clock tree inference (marginal and joint maximum likelihood)
- inference of GTR models
- rerooting to obtain best root-to-tip regression
- auto-correlated relaxed molecular clock (with normal prior)
This package contains example scripts and data to test the usage of treetime.
There are three methods to install python-treetime-examples on Ubuntu 18.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install python-treetime-examples Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install python-treetime-examples using apt-get by running the following command:
sudo apt-get -y install python-treetime-examples
Install python-treetime-examples Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install python-treetime-examples using apt by running the following command:
sudo apt -y install python-treetime-examples
Install python-treetime-examples Using aptitude
If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Ubuntu. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install python-treetime-examples using aptitude by running the following command:
sudo aptitude -y install python-treetime-examples
How To Uninstall python-treetime-examples on Ubuntu 18.04
To uninstall only the python-treetime-examples package we can use the following command:
sudo apt-get remove python-treetime-examples
Uninstall python-treetime-examples And Its Dependencies
To uninstall python-treetime-examples and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove python-treetime-examples
Remove python-treetime-examples Configurations and Data
To remove python-treetime-examples configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge python-treetime-examples
Remove python-treetime-examples configuration, data, and all of its dependencies
We can use the following command to remove python-treetime-examples configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge python-treetime-examples
References
Summary
In this tutorial we learn how to install python-treetime-examples package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
